X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3d9b68358f757f1d3c94a63b641522735c387074..dddfa30b07b2584353df378528f84945faa3ad7f:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 4ca010bab1..71e499ebca 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -42,6 +42,7 @@ import schema_salad.validate as validate
 import arvados.collection
 from .util import collectionUUID
 import ruamel.yaml as yaml
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 import arvados_cwl.arvdocker
 from .pathmapper import ArvPathMapper, trim_listing, collection_pdh_pattern, collection_uuid_pattern
@@ -168,21 +169,47 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
         #
         # Found a file, check for secondaryFiles
         #
-        primary["secondaryFiles"] = []
+        specs = []
+        primary["secondaryFiles"] = secondaryspec
         for i, sf in enumerate(aslist(secondaryspec)):
             pattern = builder.do_eval(sf["pattern"], context=primary)
             if pattern is None:
                 continue
+            if isinstance(pattern, list):
+                specs.extend(pattern)
+            elif isinstance(pattern, dict):
+                specs.append(pattern)
+            elif isinstance(pattern, str):
+                specs.append({"pattern": pattern})
+            else:
+                raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
+                    "Expression must return list, object, string or null")
+
+        found = []
+        for i, sf in enumerate(specs):
+            if isinstance(sf, dict):
+                if sf.get("class") == "File":
+                    pattern = sf["basename"]
+                else:
+                    pattern = sf["pattern"]
+                    required = sf.get("required")
+            elif isinstance(sf, str):
+                pattern = sf
+                required = True
+            else:
+                raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
+                    "Expression must return list, object, string or null")
+
             sfpath = substitute(primary["location"], pattern)
-            required = builder.do_eval(sf.get("required"), context=primary)
+            required = builder.do_eval(required, context=primary)
 
             if fsaccess.exists(sfpath):
-                primary["secondaryFiles"].append({"location": sfpath, "class": "File"})
+                found.append({"location": sfpath, "class": "File"})
             elif required:
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Required secondary file '%s' does not exist" % sfpath)
 
-        primary["secondaryFiles"] = cmap(primary["secondaryFiles"])
+        primary["secondaryFiles"] = cmap(found)
         if discovered is not None:
             discovered[primary["location"]] = primary["secondaryFiles"]
     elif inputschema["type"] not in primitive_types_set:
@@ -334,7 +361,7 @@ def upload_dependencies(arvrunner, name, document_loader,
                                  builder_job_order,
                                  discovered)
 
-    copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri)
+    copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri, checklinks=False)
     visit_class(copied, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
 
     for d in list(discovered):
@@ -392,7 +419,7 @@ def upload_dependencies(arvrunner, name, document_loader,
             discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
 
     if "$schemas" in workflowobj:
-        sch = []
+        sch = CommentedSeq()
         for s in workflowobj["$schemas"]:
             sch.append(mapper.mapper(s).resolved)
         workflowobj["$schemas"] = sch
@@ -424,17 +451,22 @@ def packed_workflow(arvrunner, tool, merged_map):
     A "packed" workflow is one where all the components have been combined into a single document."""
 
     rewrites = {}
-    packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]),
-                  tool.tool["id"], tool.metadata, rewrite_out=rewrites)
+    packed = pack(arvrunner.loadingContext, tool.tool["id"],
+                  rewrite_out=rewrites,
+                  loader=tool.doc_loader)
 
     rewrite_to_orig = {v: k for k,v in viewitems(rewrites)}
 
     def visit(v, cur_id):
         if isinstance(v, dict):
             if v.get("class") in ("CommandLineTool", "Workflow"):
-                if "id" not in v:
-                    raise SourceLine(v, None, Exception).makeError("Embedded process object is missing required 'id' field")
-                cur_id = rewrite_to_orig.get(v["id"], v["id"])
+                if tool.metadata["cwlVersion"] == "v1.0" and "id" not in v:
+                    raise SourceLine(v, None, Exception).makeError("Embedded process object is missing required 'id' field, add an 'id' or use to cwlVersion: v1.1")
+                if "id" in v:
+                    cur_id = rewrite_to_orig.get(v["id"], v["id"])
+            if "path" in v and "location" not in v:
+                v["location"] = v["path"]
+                del v["path"]
             if "location" in v and not v["location"].startswith("keep:"):
                 v["location"] = merged_map[cur_id].resolved[v["location"]]
             if "location" in v and v["location"] in merged_map[cur_id].secondaryFiles:
@@ -578,7 +610,8 @@ class Runner(Process):
     """Base class for runner processes, which submit an instance of
     arvados-cwl-runner and wait for the final result."""
 
-    def __init__(self, runner, tool, loadingContext, enable_reuse,
+    def __init__(self, runner, updated_tool,
+                 tool, loadingContext, enable_reuse,
                  output_name, output_tags, submit_runner_ram=0,
                  name=None, on_error=None, submit_runner_image=None,
                  intermediate_output_ttl=0, merged_map=None,
@@ -587,10 +620,9 @@ class Runner(Process):
                  collection_cache_is_default=True):
 
         loadingContext = loadingContext.copy()
-        loadingContext.metadata = loadingContext.metadata.copy()
-        loadingContext.metadata["cwlVersion"] = INTERNAL_VERSION
+        loadingContext.metadata = updated_tool.metadata.copy()
 
-        super(Runner, self).__init__(tool.tool, loadingContext)
+        super(Runner, self).__init__(updated_tool.tool, loadingContext)
 
         self.arvrunner = runner
         self.embedded_tool = tool